A method of controlling polishing includes polishing a substrate at a first polishing station, monitoring the substrate with a first eddy current monitoring system to generate a first signal, determining an ending value of the first signal for an end of polishing of the substrate at the first polishing station, determining a first temperature at the first polishing station, polishing the substrate at a second polishing station, monitoring the substrate with a second eddy current monitoring system to generate a second signal, determining a starting value of the second signal for a start of polishing of the substrate at the second polishing station, determining a gain for the second polishing station based on the ending value, the starting value and the first temperature, and calculating a third signal based on the second signal and the gain.